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On Linux, /dev/std{in,out,err} don’t connect to devices, they give access to each process’ corresponding file descriptors. See the output of ls -l /dev/std*: lrwxrwxrwx. 1 root root 15 Feb 24 09:34 /dev/stderr -> /proc/self/fd/2 lrwxrwxrwx. 1 root root 15 Feb 24 09:34 /dev/stdin -> /proc/self/fd/0 lrwxrwxrwx. 1 root root 15 Feb 24 09:34 /dev/stdout -&...


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Just using nohup without any redirection the file nohup.out is written in append mode. That's why the truncation of the file after inspection by the command > nohup.out sets the file to length zero and subsequent output of the program is written to nohup.out at the start of the file. That is exactly what the above answer to the question told - and it ...


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It depends on how reformat.sh is written. Often UNIX commands will use stdin and stdout if you do not give them any input/output: reformat.sh in=test.bam primaryonly | reformat.sh out1=r1.fq.gz out2=r2.fq.gz interleaved addcolon Other times they will accept - as a file name: reformat.sh in=test.bam out=- primaryonly | reformat.sh in=- out1=r1.fq.gz ...


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You are getting very confused with file-name-extensions. There is no such thing. Not since MS-DOS and CPM. Microsoft's Windows still uses them to trigger actions in file-explorer, but they are just part of the file-name. Therefore stdout and stdout.fq are different files. Also the name for stdout is /dev/stdout, and stdin is /dev/stdin


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